docs(scn): status — track complete (SV/CNV/render/contrast)#397
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Update the SCN status doc to reflect completion: SV + CNV models built for both strains and rendered end-to-end (loop closed), the MM26-vs-PA3/BD3 contrast with its confound caveat, the RDCN→INFO/CN CNV format gap + fix, and the v1.20.1 RNG release. Refreshed tooling table, Delta ops notes (strain-override + verify-the-statistic), and the open items (common-reference comparison, Phase 2, harness #395, CNV biology, long reads). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Per-strain sim-vs-truth fidelity is the validation goal and stands on its own regardless of reference; the strain contrast + common-reference run are a biological virulence claim on top of the validated tool, not a validation gap. Reframe "Open / next steps" to separate tooling/validation items that can proceed (Phase 2 AF replay, harness #395) from biology extensions parked pending colleague feedback (common-ref comparison, CNV sanity, long reads). Co-Authored-By: Claude <noreply@anthropic.com>
Trace the alt-fraction mechanism end-to-end on develop. Corrects stale line numbers and identifies the real lever: the per-read alt/ref branch in generate_read (fastq_tools.rs:462), which drives both emitted reads and the AdCounter (so golden AF tracks it for free). mutate_position is a secondary SV-junction-only path. Input-VCF variants confirmed to flow through the main path via variant_map. Scope reduced to: add Variant.allele_fraction, populate in from_file (INFO/AF or FORMAT/AD), generalize the :462 branch; no golden-VCF output change needed. Notes overlap with parked polyploidy #266. Co-Authored-By: Claude <noreply@anthropic.com>
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Brings
docs/scn_status.mdup to date now that the planned SCN track is complete:SVTYPE=CNV); notes theRDCN→INFO/CNformat gap + the lift that fixes it.Doc only.
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